GSEA single cell

Question

[SHP]

Hello, I am analyzing single cell data. I ran Seurat's FindMarkers function to find the differentially expressed genes between each diseased and healthy celltype. I wanted to do Gene set enrichment analysis using clusterProfiler package. How to rank genes before using it.

[Ming Tommy Tang]

I use sign(log2Fold )* -log10(pvalue), if you use presto you may use auc to rank, see https://crazyhottommy.github.io/scRNA-seq-workshop-Fall-2019/scRNAseq_workshop_3.html

Answer 1

[Ribo]

Hi,

If you are interested in the magnitude of change, you can use the log2 fold-change values for ranking.